earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Package details

AuthorThibaut Jombart [aut, cre], Anne Cori [aut], Pierre Nouvellet [aut], Janetta Skarp [aut], Zhian N. Kamvar [ctb], Tim Taylor [ctb] (<https://orcid.org/0000-0002-8587-7113>)
MaintainerThibaut Jombart <thibautjombart@gmail.com>
LicenseMIT + file LICENSE
URL https://www.repidemicsconsortium.org/earlyR/
Package repositoryView on CRAN
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earlyR documentation built on Oct. 27, 2020, 9:07 a.m.